Abstract
Analyzing cell differentiation during development in a complex organism requires the analysis of expression and chromatin profiles in individual cell types. Our laboratory has developed a simple and generally applicable strategy to purify specific cell types from whole organisms for simultaneous analysis of chromatin and expression. The method, termed INTACT for Isolation of Nuclei TAgged in specific Cell Types, depends on the expression of an affinity-tagged nuclear envelope protein in the cell type of interest. These nuclei can be affinity-purified from the total pool of nuclei and used as a source for RNA and chromatin. The method serves as a simple and scalable alternative to FACS sorting or laser capture microscopy to circumvent the need for expensive equipment and specialized skills. This chapter provides detailed protocols for the cell-type specific purification of nuclei from Caenorhabditis elegans.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Ng RK, Gurdon JB (2008) Epigenetic inheritance of cell differentiation status. Cell Cycle 7:1173–1177
Yuan G, Zhu B (2012) Histone variants and epigenetic inheritance. Biochim Biophys Acta 1819:222–229
Azuara V, Perry P, Sauer S et al (2006) Chromatin signatures of pluripotent cell lines. Nat Cell Biol 8:532–538
Fox RM, Watson JD, Von Stetina SE et al (2007) The embryonic muscle transcriptome of Caenorhabditis elegans. Genome Biol 8:R188
Miller MR, Robinson KJ, Cleary MD, Doe CQ (2009) TU-tagging: cell type-specific RNA isolation from intact complex tissues. Nat Methods 6:439–441
Roy PJ, Stuart JM, Lund J, Kim SK (2002) Chromosomal clustering of muscle-expressed genes in Caenorhabditis elegans. Nature 418:975–979
Bonn S, Zinzen RP, Girardot C et al (2012) Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development. Nat Genet 44:148–156
Bonn S, Zinzen RP, Perez-Gonzalez A et al (2012) Cell type-specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP. Nat Protoc 7:978–994
Fox RM, Von Stetina SE, Barlow SJ et al (2005) A gene expression fingerprint of C. elegans embryonic motor neurons. BMC Genomics 6:42
Sugiyama T, Rodriguez RT, McLean GW et al (2007) Conserved markers of fetal pancreatic epithelium permit prospective isolation of islet progenitor cells by FACS. Proc Natl Acad Sci U S A 104:175–180
Von Stetina SE, Watson JD, Fox RM et al (2007) Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system. Genome Biol 8:R135
Haenni S, Ji Z, Hoque M et al (2012) Analysis of C. elegans intestinal gene expression and polyadenylation by fluorescence-activated nuclei sorting and 3'-end-seq. Nucleic Acids Res 40:6304–6318
Southall TD, Gold KS, Egger B et al (2013) Cell-type-specific profiling of gene expression and chromatin binding without cell isolation: assaying RNA Pol II occupancy in neural stem cells. Dev Cell 26:101–112
Burgemeister R (2011) Laser capture microdissection of FFPE tissue sections bridging the gap between microscopy and molecular analysis. Methods Mol Biol 724:105–115
Erickson HS, Albert PS, Gillespie JW, Rodriguez-Canales J, Marston Linehan W, Pinto PA et al (2009) Quantitative RT-PCR gene expression analysis of laser microdissected tissue samples. Nat Protoc 4:902–922
Golubeva Y, Salcedo R, Mueller C et al (2013) Laser capture microdissection for protein and NanoString RNA analysis. Methods Mol Biol 931:213–257
Neira M, Azen E (2002) Gene discovery with laser capture microscopy. Methods Enzymol 356:282–289
Rabien A (2010) Laser microdissection. Meth Mol Biol 576:39–47
Deal RB, Henikoff S (2010) A simple method for gene expression and chromatin profiling of individual cell types within a tissue. Dev Cell 18:1030–1040
Deal RB, Henikoff S (2011) The INTACT method for cell type-specific gene expression and chromatin profiling in Arabidopsis thaliana. Nat Protoc 6:56–68
Steiner FA, Talbert PB, Kasinathan S et al (2012) Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling. Genome Res 22:766–777
Amin NM, Greco TM, Kuchenbrod LM et al (2014) Proteomic profiling of cardiac tissue by isolation of nuclei tagged in specific cell types (INTACT). Development 141:962–973
Henry GL, Davis FP, Picard S et al (2012) Cell type-specific genomics of Drosophila neurons. Nucleic Acids Res 40:9691–9704
Acknowledgements
This work was supported by HHMI, NIH (U01-HG004274), and the Swiss National Science Foundation (PBSKP3-124362).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer Science+Business Media New York
About this protocol
Cite this protocol
Steiner, F.A., Henikoff, S. (2015). Cell Type-Specific Affinity Purification of Nuclei for Chromatin Profiling in Whole Animals. In: Hancock, R. (eds) The Nucleus. Methods in Molecular Biology, vol 1228. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1680-1_1
Download citation
DOI: https://doi.org/10.1007/978-1-4939-1680-1_1
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-1679-5
Online ISBN: 978-1-4939-1680-1
eBook Packages: Springer Protocols